[BioC] 'Rsamtools' produces segfaults with XS tag

[Misha Kapushesky]

Hi,

Thanks for the speedy fix!

--Misha

On Fri, 13 Aug 2010, Martin Morgan wrote:

> On 8/13/2010 2:11 PM, Misha Kapushesky wrote:
>> Hi,
>> 
>> I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. 
>> After some more tinkering - it seems I can't reproduce this on my Mac, only 
>> on our Linux install. I also just noticed that the released version is 
>> 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps it's 
>> a version incompatibility and we managed to install ourselves something 
>> incompatible? If that's the case, we'll probably try to get a more standard 
>> install going, and hopefully the problem will go away...
>> 
>
> This should be fixed in 1.0.8 (release) or 1.1.12 (devel), available via 
> biocLite in the next several days or via svn 
> (http://bioconductor.org/developers/source-control/) immediately.
>
> Thanks for the report and sample data.
>
> Martin
>
>> --Misha
>> 
>> On Fri, 13 Aug 2010, Martin Morgan wrote:
>> 
>>> Thanks Misha for the additional hints; I looked at the code and couldn't
>>> see anything immediately wrong, but if you can provide a (minimal?)  bam
>>> file displaying the problem that would be helpful. Martin
>>> 
>>> Misha Kapushesky <ostolop at ebi.ac.uk> writes:
>>> 
>>>> Hi,
>>>> 
>>>> I can add more detail to this - the same problem:
>>>> 
>>>>> library( "Rsamtools" )
>>>> ...
>>>>> tags <- c("NM", "MD", "XA", "XS","NS")
>>>>> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam"
>>>>> and_bam = scanBam(and_file, param = ScanBamParam(flag = 
>>>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags))
>>>> 
>>>> *** caught segfault ***
>>>> address 0x2b3449beb8cd, cause 'invalid permissions'
>>>> 
>>>> Traceback:
>>>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...)
>>>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = 
>>>> param)
>>>> 3: scanBam(and_file, param = ScanBamParam(flag = 
>>>> scanBamFlag(isUnmappedQuery = FALSE),     tag = tags))
>>>> 4: scanBam(and_file, param = ScanBamParam(flag = 
>>>> scanBamFlag(isUnmappedQuery = FALSE),     tag = tags))
>>>> 
>>>> This error goes away if we don't include "XS" in tags, also if we use
>>>> version 1.0.0 of Rsamtools. Any ideas?
>>>> 
>>>> The sessionInfo() output is below. Thanks in advance!
>>>> 
>>>> --Misha
>>>> 
>>>>> sessionInfo()
>>>> R version 2.11.1 (2010-05-31)
>>>> x86_64-unknown-linux-gnu
>>>> 
>>>> locale:
>>>> [1] C
>>>> 
>>>> attached base packages:
>>>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>>>> [8] base
>>>> 
>>>> other attached packages:
>>>> [1] Rsamtools_1.1.11    Biostrings_2.16.9   GenomicRanges_1.0.7
>>>> [4] IRanges_1.6.11      svMisc_0.9-57       JavaGD_0.5-2
>>>> [7] rJava_0.8-4
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] Biobase_2.8.0
>>>> 
>>>> 
>>>> On Thu, 12 Aug 2010, Andrew Tikhonov wrote:
>>>> 
>>>>> Dear Biocore Team,
>>>>>
>>>>>     We've got a problem where 'Rsamtools' produces segfaults and
>>>>> core-dumps when reading a .bam file using the "XS" tag. We have a
>>>>> faulty .bam and the list or R commands to reproduce it. Could you
>>>>> please point us to someone who we may discuss this matter with and,
>>>>> if possible, fix the problem.
>>>>>
>>>>>     Thanks a lot in advance.
>>>>> 
>>>>> Regards,
>>>>> Andrew
>>>>> 
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>>>> 
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>>> 
>>> -- 
>>> Martin Morgan
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>> 
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>> 
>